Matt Thanks. Yes I can wait for a few weeks/months (its only a local memory footprint issue and in no way hampers my ability to solve problems).
Btw just for curiosity are you using the same technique discussed by Barry? Maybe I am overlooking something trivial in his post. Tabrez On Jan 27, 2012, at 10:26 AM, Matthew Knepley wrote: > On Fri, Jan 27, 2012 at 10:32 AM, Tabrez Ali > <stali at geology.wisc.edu> wrote: > PETSc Gurus > > First I want to thank you for patiently answering questions that I > have asked in past regarding preallocation. Unfortunately I am still > having problems. > > I have a small unstructured FE (elasticity) code that uses PETSc. > > Unfortunately I am not yet able to find an _efficient_ way of > calculating the non-zero structure so I simply overestimate the o_nz > and d_nz values (= dimension x max_number_of nodes > _a_node_contributes_to) which means that my stiffness matrix > consumes at least 2X more memory. For example, for a perfectly > structured mesh of linear hexes this number is 3*27=81=o_nz=d_nz. In > complicated 3D linear tet/hex meshes that I have generated I rarely > need to set a value greater than 150. In general I have found that > as long as I keep DOF/core between 100-200K (assuming 1GB/per core) > there is enough local RAM left even when memory for stiffness matrix > is overestimated by 2X-6X. > > In any case now I do want to preallocate exactly for better memory > performance and the ambiguity involved in choosing a reasonable o_nz/ > d_nz. The way I am trying to do it involves loops like ... > > do i=1, num_local_elements > do j=1, num_total_nodes > ... > end do > end do > > or using lists that involve searches. > > This unfortunately takes much time (much more than assembly and > solve) due to the second loop. I am aware of many posts/slides by > PETSc authors that mention that the non-zero structure can be found > simply by looping once through elements but what to do next is not > quite clear. > > I am also aware of this post by Barry [ > http://lists.mcs.anl.gov/pipermail/petsc-users/2008-May/003020.html > ] but I cannot get it to work for a simple 4 element problem. Can > some one please expand on the strategy being suggested by Barry > specially where the loops are discussed (I understand the arrays and > the vecscatter part). I am also not sure how does using a t of 0.5 > and 1 prevents double counting. Shouldn't it be 0 and 1? > > I am also aware of some capabilities in DMMESH but right now I dont > understand it well enough to utilize it. > > I agree with you here. Its not easy enough to use. However, I have > rewritten the basics of it completely in C, which > will all have easy Fortran bindings. You can specify your mesh with > adjacency lists using Fortran arrays. The last part > I am working on is matrix preallocation. I would not normally ask > you to wait, but I think I am pretty close. Mail me > directly if you want more info. I think it should only take me a few > weeks to finish. > > Thanks, > > Matt > > Alternatively does PETSc support MATMPIAIJ of size=integer(1)/ > logical instead of real(8) which I can use to put zeros/ones (when I > loop over elements the first time) to get the non-zero structure? > > Thanks in advance. > > Tabrez > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which > their experiments lead. > -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120127/9a0fc393/attachment.htm>
